Nové poznámky (py_gmm)

Former-commit-id: 9e7cd43e6219e5f25d4bcd8d116b68712db97fe5

dipdip.bib

@@ -13,6 +13,10 @@
 	month = aug,
 	year = {2004},
 	pages = {643--662},
+	annote = {Richardson's fermion pairing model solution (1-3) and Gaudin magnet (12).
+Neither of the models is general enough for our case: Gaudin model does not include the bosonic part.
+Section II.D contains generalized Richardson-Gaudin models. It is unlikely that they can be mapped to our model.
+The PRL 86 5172 reference (spin glasses) does not include the bosonic mode, either.},
 	file = {APS Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/AK9BACU6/RevModPhys.76.html:text/html;RevModPhys.76.643.pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/I5NMPRJR/RevModPhys.76.643.pdf:application/pdf}
 }
 
@@ -46,11 +50,24 @@
 	month = may,
 	year = {2000},
 	pages = {062309},
+	annote = {Just two atoms, also multilevel.},
 	file = {APS Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/DNA7CFVV/PhysRevA.61.html:text/html;get (3).pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/PNT2X2MD/get (3).pdf:application/pdf}
 }
 
 @techreport{_marek:things_????,
 	title = {Marek:{Things} to do 31.4.2015},
+	annote = {
+Effects of randomness: try some gradual transition from ordered /aligned case to random.
+Scaling effects.
+✓Compare the parameters in the model to other relevant quantities in the system (e.g. temperature). Think about reasonable cutoffs.
+✓Usefulness of the full coupling model: compare to nearest neighbour coupling.
+Dark states, phase of the dipoles.
+Predictions for real systems: think about what results could be observable in experiments, and how.
+
+Addenda 12. 5. 2015
+✓Concentrations: Can they be high enough to get non-negligible effects?
+Investigate the non-trivial dependence of band width on direction randomness.
+✓Divergences in coupling of close molecules – can this be a real effect?},
 	file = {2015-5_concentration.pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/7HJWUKS7/2015-5_concentration.pdf:application/pdf;2015-5_wrk.pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/RBERG7T8/2015-5_wrk.pdf:application/pdf}
 }
 
@@ -67,6 +84,8 @@
 	month = may,
 	year = {2015},
 	pages = {196402},
+	annote = {Lindblad master equation simulation (in QuTiP) of a 1D chain of  two-level systems (with d-d coupling) + single cavity mode. The chains should correspond to J-aggregates, if I understand correctly.
+They observe exciton conductance (defined as loss of energy from the last molecule per driving power) as a function of collective Rabi frequancy (between molecules and cavity).},
 	file = {APS Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/P9V3J9WM/PhysRevLett.114.html:text/html;PhysRevLett.114.196402.pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/6AJT5WQP/PhysRevLett.114.196402.pdf:application/pdf}
 }
 
@@ -181,6 +200,9 @@
 	month = jan,
 	year = {1973},
 	pages = {1--121},
+	annote = {Cf. page 11 for references on Power-Zienau-Wooley transform.
+ A recent paper by Woolley [255] showsthat the integral (1.39) contains the binding energies (1.41) within the molecules only but nointermolecular Coulomb terms. Only higher order terms give intermolecular forces in a well knownway, see the monograph by Marganau and Kestner [147].
+ },
 	file = {ScienceDirect Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/22K5U5CP/0370157373900112.html:text/html;stenholm1973.pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/4XMK5NJZ/stenholm1973.pdf:application/pdf}
 }
 
@@ -284,6 +306,9 @@
 	year = {2007},
 	keywords = {03.60.Nk, 03.80.+r, 34.80.-i, Optical Spectroscopy, Ultrafast Optics},
 	pages = {291--299},
+	annote = {
+Constant interaction between two-level systems
+},
 	file = {Operator method for calculating the spectrum of states in the framework of the_Boyarshinova_Feranchuk_2007.pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/SA4ARTGA/Operator method for calculating the spectrum of states in the framework of the_Boyarshinova_Feranchuk_2007.pdf:application/pdf;Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/FPZWZNB3/10.html:text/html}
 }
 
@@ -300,6 +325,9 @@
 	month = oct,
 	year = {2004},
 	pages = {153001},
+	annote = {
+Experimental paper with Rydberg atoms
+},
 	file = {Angular Dependence of the Dipole-Dipole Interaction in a Nearly One-Dimensional_Carroll_2004.pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/SFVRKKCP/Angular Dependence of the Dipole-Dipole Interaction in a Nearly One-Dimensional_Carroll_2004.pdf:application/pdf;APS Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/NAJSQXHT/PhysRevLett.93.html:text/html}
 }
 
@@ -318,6 +346,10 @@
 	year = {2005},
 	keywords = {Dipole–dipole interaction, Exact solution, Extended Dicke model},
 	pages = {94--100},
+	annote = {
+Bethe ansatz solution for extended Dicke model
+Constant interaction between two-level systems
+},
 	file = {Exact solutions of an extended Dicke model_Pan_2005.pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/JG72Q9QW/Exact solutions of an extended Dicke model_Pan_2005.pdf:application/pdf;ScienceDirect Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/X6XWWFCH/S0375960105006614.html:text/html}
 }
 
@@ -334,6 +366,10 @@
 	month = nov,
 	year = {1990},
 	pages = {5695--5702},
+	annote = {
+Question: how does dipole-dipole interaction change spontaneous emission from two emitters in overdamped cavity?
+This paper is by Leonardi who was also author in the Riv. Nuovo Cimento paper that we don't have access to. Maybe this contains some of the same results?
+},
 	file = {APS Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/NJM2AS9V/PhysRevA.42.html:text/html;Dipole-dipole interaction and spontaneous decay of two atoms in an overdamped_Seminara_Leonardi_1990.pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/ZP6V9P97/Dipole-dipole interaction and spontaneous decay of two atoms in an overdamped_Seminara_Leonardi_1990.pdf:application/pdf}
 }
 
@@ -350,6 +386,9 @@
 	month = feb,
 	year = {1996},
 	pages = {1320--1323},
+	annote = {This seems to be the only paper having the general form of the Hamiltonian and randomly placed dipoles.
+ 
+ },
 	file = {APS Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/RS6CEKV4/PhysRevLett.76.html:text/html;PhysRevLett.76.1320.pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/6R3PPWCX/PhysRevLett.76.1320.pdf:application/pdf}
 }
 
@@ -364,6 +403,8 @@
 	month = feb,
 	year = {2001},
 	keywords = {Science / Physics / Atomic \& Molecular, Science / Physics / General, Science / Physics / Nuclear, Science / Physics / Quantum Theory, Science / Weights \& Measures, Technology \& Engineering / Measurement},
+	annote = {Section 4.3 (p. 402+) might be worth checking
+and 3.4 (p, 389+) too.},
 	file = {[R._Kaiser,_C._Westbrook,_F._David]_Coherent_atomi(BookZZ.org).pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/BCZECWMX/[R._Kaiser,_C._Westbrook,_F._David]_Coherent_atomi(BookZZ.org).pdf:application/pdf}
 }
 
@@ -523,6 +564,7 @@
 	year = {2015},
 	note = {arXiv: 1502.04905},
 	keywords = {Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Optics},
+	annote = {Comment: 5 pages, 3 figures},
 	file = {arXiv\:1502.04905 PDF:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/JGBF9C8E/Gonzalez-Ballestero et al. - 2015 - Harvesting Excitons Through Plasmonic Strong Coupl.pdf:application/pdf;arXiv.org Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/JSQQKKRZ/1502.html:text/html}
 }
 
@@ -857,6 +899,7 @@
 	month = feb,
 	year = {2012},
 	pages = {075303},
+	annote = {The formula (A1) for spherical Green's function is incorrect!},
 	file = {APS Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/N7X9U595/PhysRevB.85.html:text/html;PhysRevB.85.075303(1).pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/VST7NAFK/PhysRevB.85.075303(1).pdf:application/pdf}
 }
 
@@ -1064,6 +1107,45 @@ Cross-referenced as UMIACS-TR-2001-44},
 	file = {josaa-24-6-1695.pdf:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/33I3IGX6/josaa-24-6-1695.pdf:application/pdf}
 }
 
+@article{pellegrini_interacting_2007,
+	series = {{EMRS} 2006 {Symposium} {A}: {Current} {Trends} in {Nanoscience} - from {Materials} to {Applications}},
+	title = {Interacting metal nanoparticles: {Optical} properties from nanoparticle dimers to core-satellite systems},
+	volume = {27},
+	issn = {0928-4931},
+	shorttitle = {Interacting metal nanoparticles},
+	url = {http://www.sciencedirect.com/science/article/pii/S0928493106002657},
+	doi = {10.1016/j.msec.2006.07.025},
+	abstract = {Prompted by the growing interest in the optical properties of coupled metal nanoclusters, we implemented a code in the framework of Generalized Multiparticle Mie theory (GMM) to simulate far-field properties of strongly interacting spherical particles. In order to validate the code different case studies, including systems modeled for the first time, have been treated. The extinction properties of noble metal nanocluster dimers, chains and core-satellite structures have been computed. Influence of parameters like interparticle distance, incident field polarization, number of multipolar expansions and chain length has been studied. The code provided reliable results in agreement with previous works and proved to be affordable and robust in any of the treated case.},
+	number = {5–8},
+	urldate = {2015-11-18},
+	journal = {Materials Science and Engineering: C},
+	author = {Pellegrini, G. and Mattei, G. and Bello, V. and Mazzoldi, P.},
+	month = sep,
+	year = {2007},
+	keywords = {Coupled plasmons, Interacting nanoparticles, Optical properties},
+	pages = {1347--1350},
+	file = {ScienceDirect Full Text PDF:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/77R8E8NQ/Pellegrini et al. - 2007 - Interacting metal nanoparticles Optical propertie.pdf:application/pdf;ScienceDirect Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/IXCSKSFT/S0928493106002657.html:text/html}
+}
+
+@article{xu_efficient_1998,
+	title = {Efficient {Evaluation} of {Vector} {Translation} {Coefficients} in {Multiparticle} {Light}-{Scattering} {Theories}},
+	volume = {139},
+	issn = {0021-9991},
+	url = {http://www.sciencedirect.com/science/article/pii/S0021999197958678},
+	doi = {10.1006/jcph.1997.5867},
+	abstract = {Vector addition theorems are a necessary ingredient in the analytical solution of electromagnetic multiparticle-scattering problems. These theorems include a large number of vector addition coefficients. There exist three basic types of analytical expressions for vector translation coefficients: Stein's (Quart. Appl. Math.19, 15 (1961)), Cruzan's (Quart. Appl. Math.20, 33 (1962)), and Xu's (J. Comput. Phys.127, 285 (1996)). Stein's formulation relates vector translation coefficients with scalar translation coefficients. Cruzan's formulas use the Wigner 3jm symbol. Xu's expressions are based on the Gaunt coefficient. Since the scalar translation coefficient can also be expressed in terms of the Gaunt coefficient, the key to the expeditious and reliable calculation of vector translation coefficients is the fast and accurate evaluation of the Wigner 3jm symbol or the Gaunt coefficient. We present highly efficient recursive approaches to accurately evaluating Wigner 3jm symbols and Gaunt coefficients. Armed with these recursive approaches, we discuss several schemes for the calculation of the vector translation coefficients, using the three general types of formulation, respectively. Our systematic test calculations show that the three types of formulas produce generally the same numerical results except that the algorithm of Stein's type is less accurate in some particular cases. These extensive test calculations also show that the scheme using the formulation based on the Gaunt coefficient is the most efficient in practical computations.},
+	number = {1},
+	urldate = {2015-11-18},
+	journal = {Journal of Computational Physics},
+	author = {Xu, Yu-lin},
+	month = jan,
+	year = {1998},
+	pages = {137--165},
+	annote = {N.B. erratum regarding eqs (50,52,53)
+http://www.sciencedirect.com/science/article/pii/S0021999197956874},
+	file = {ScienceDirect Full Text PDF:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/STV5263F/Xu - 1998 - Efficient Evaluation of Vector Translation Coeffic.pdf:application/pdf;ScienceDirect Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/VMGZRSAA/S0021999197958678.html:text/html}
+}
+
 @article{moneda_dyadic_2007-2,
 	title = {Dyadic {Green}'s function of a cluster of spheres},
 	volume = {24},
@@ -1222,6 +1304,13 @@ Cross-referenced as UMIACS-TR-2001-44},
 	year = {2015}
 }
 
+@misc{pellegrini_py_gmm_2015,
+	title = {py\_gmm},
+	url = {https://github.com/gevero/py_gmm},
+	author = {Pellegrini, Giovanni},
+	year = {2015}
+}
+
 @article{blake_surface_2015,
 	title = {Surface plasmon-polaritons in periodic arrays of {V}-grooves strongly coupled to quantum emitters},
 	url = {http://arxiv.org/abs/1504.00938},
@@ -1233,5 +1322,6 @@ Cross-referenced as UMIACS-TR-2001-44},
 	year = {2015},
 	note = {arXiv: 1504.00938},
 	keywords = {Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Optics},
+	annote = {Comment: 17 pages, 6 figures, submitted to Phys. Rev. B},
 	file = {arXiv\:1504.00938 PDF:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/INXMWNEH/Blake and Sukharev - 2015 - Surface plasmon-polaritons in periodic arrays of V.pdf:application/pdf;arXiv.org Snapshot:/home/necadam1/.zotero/zotero/9uf64zmd.default/zotero/storage/TIMEX8TF/1504.html:text/html}
 }

misc/subroutines-mstm

@@ -53,7 +53,7 @@ external_to_internal_expansion #
 m1_to_the_n # sign flipped for odd degrees
 rottranfarfield # far field formula for outgoing vswf translation
 farfieldtranslationerror # correction ter for hybrid bcgm solution
-rottran # the vectorized rotation translation-rotation operation
+rottran # the vectorized rotation translation-rotation operation !!!!	
 spheregaussianbeamcoef # GB coefficients for sphere-centered expansion, obtained via translation
 rotvec # rotation of expansion coefficients amn by euler angles
 

worknotes.lyx

@@ -198,6 +198,10 @@ reference "sub:SCUFF-TMATRIX"
 Available software
 \end_layout
 
+\begin_layout Itemize
+TODO which of them can calculate the VSWF translation coefficients?
+\end_layout
+
 \begin_layout Subsection
 SCUFF-EM 
 \begin_inset CommandInset citation
@@ -424,7 +428,21 @@ Options for random orientation calculations
 \begin_inset Quotes erd
 \end_inset
 
-? 
+? Well, it seems that for fixed orientation, it is not possible to specify
+ the T-matrix, cf.
+ the description of 
+\family typewriter
+fixed_or_random_orientation
+\family default
+ option in 
+\begin_inset CommandInset citation
+LatexCommand cite
+after "3.2.3"
+key "mackowski_mstm_2013"
+
+\end_inset
+
+.
 \end_layout
 
 \begin_layout Subsubsection
@@ -432,7 +450,11 @@ Interesting subroutines
 \end_layout
 
 \begin_layout Itemize
-rottranfarfield: it states 
+
+\family typewriter
+rottranfarfield
+\family default
+: it states 
 \begin_inset Quotes eld
 \end_inset
 
@@ -444,10 +466,181 @@ far field formula for outgoing vswf translation
  What is that and how does it differ from whatever else (near field?) formula?
 \end_layout
 
-\begin_layout Itemize
+\begin_layout Subsection
+py_gmm
+\begin_inset CommandInset citation
+LatexCommand cite
+key "pellegrini_py_gmm_2015"
+
+\end_inset
+
 
 \end_layout
 
+\begin_layout Itemize
+Fortran code, already (partially) pythonized using 
+\family typewriter
+f2py
+\family default
+ by the authors(?); under GNU GPLv3.
+ This could save my day.
+\end_layout
+
+\begin_layout Itemize
+Lots of unnecessary code duplication (see e.g.
+ 
+\family typewriter
+coeff_sp2
+\family default
+ and 
+\family typewriter
+coeff_sp2_dip
+\family default
+ subroutines).
+\end_layout
+
+\begin_layout Itemize
+Has comments!!! (Sometimes they are slightly inaccurate due to the copy-pasting,
+ but it is still one of the most readable FORTRAN codes I have seen.)
+\end_layout
+
+\begin_layout Itemize
+The subroutines seem not to be bloated with dependencies on static/global
+ variables, so they should be quite easily reusable.
+\end_layout
+
+\begin_layout Itemize
+The FORTRAN code was apparently used in 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "pellegrini_interacting_2007"
+
+\end_inset
+
+.
+ Uses the multiple-scattering formalism described in 
+\begin_inset CommandInset citation
+LatexCommand cite
+key "xu_efficient_1998"
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Subsubsection
+Interesting subroutines
+\end_layout
+
+\begin_layout Standard
+Mie scattering:
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+coeff_sp2
+\family default
+: calculation of the Mie scattering coefficients (
+\begin_inset Formula $\overline{a}_{n}^{l},\overline{b}_{n}^{l}$
+\end_inset
+
+ as in 
+\begin_inset CommandInset citation
+LatexCommand cite
+after "(1), (2), \\ldots"
+key "pellegrini_py_gmm_2015"
+
+\end_inset
+
+), for a set of spheres (therefore all the parameters have +1 dimension).
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+What does the input parameter 
+\family typewriter
+v_req
+\family default
+ (
+\emph on
+vettore raggi equivalenti
+\emph default
+) mean?
+\end_layout
+
+\begin_layout Itemize
+How do I put in the environment permittivity?
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+m_epseq
+\family default
+ are real and imaginary parts of the permittivity (which are then transformed
+ into complex 
+\family typewriter
+v_epsc
+\family default
+)
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+ref_index
+\family default
+ is the environment refractive index (called 
+\family typewriter
+n_matrix 
+\family default
+in the example ipython notebook)
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+v_req
+\family default
+ are the sphere radii?
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+nstop
+\family default
+ is the maximum order of the 
+\begin_inset Formula $n$
+\end_inset
+
+-expansion
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+neq
+\family default
+ is ns, number of spheres for which the calculation is performed apparently,
+ it is connected to some 
+\begin_inset Quotes eld
+\end_inset
+
+dirty hack to interface fortran and python properly
+\begin_inset Quotes erd
+\end_inset
+
+ (cf.
+ 
+\family typewriter
+gmm_f2py_module.f90
+\family default
+)
+\end_layout
+
+\end_deeper
 \begin_layout Section
 Code integration
 \end_layout
@@ -690,6 +883,30 @@ switched axes
 ...
 \end_layout
 
+\begin_layout Standard
+If I set the dipole reflection coefficients RH[1], RV[1] to zero, and multiply
+ the the quadrupole reflection coefficients RH[2], RV[2] by 
+\begin_inset Formula $10^{6}$
+\end_inset
+
+, the peak at 
+\begin_inset Formula $3.0\,\mathrm{eV}$
+\end_inset
+
+ dissapears and a tiny(!) peak appears around the (expected) position of
+ 
+\begin_inset Formula $3.0\,\mathrm{eV}$
+\end_inset
+
+.
+ Have I fucked up the Mie reflection coefficients? Sounds like if I forgot
+ a factor of 
+\begin_inset Formula $c$
+\end_inset
+
+ somewhere.
+\end_layout
+
 \begin_layout Subsection
 Delga JoO 
 \begin_inset CommandInset citation